I think the question is answered rather easily (if not satisfyingly) by making the fair assumption that the writers just kept pulling villains out of their asses.

It's clear the Fallen didn't exist before the second movie. It's also rather strange that no one mentioned Transformers being found in the 1960's in the first two movies. You would think that would have come up at some point. They didn't plan anything out for the franchise. It's just bad writing.

Actually the Fallen was a major Transformer character in the world of transformers, he never appeared in the show but he was a big part of the comics that explains their history and he is one of the original 12 transformers and the very first decepticon. I'm not sure if sentinal prime was ever in the show but he too was a big part of the comics and lure of transformers.